We present semi-empirical model chromospheres computed with the atmosphere code PHOENIX. The models are designed to fit the observed spectra of five mid- to late-type M dwarfs. Next to hydrogen lines from the Balmer series we used various metal lines, e.g. from Fe i, for the comparison between data and models. Our computations show that an NLTE treatment of C, N, O impacts on the hydrogen line formation, while NLTE treatment of less abundant metals such as nickel influences the lines of the considered species itself. For our coolest models we investigated also the influence of dust on the chromospheres and found that dust increases the emission line flux. Moreover we present an (electronically published) emission line list for the spectral range of 3100 to 3900 and 4700 to 6800 Å for a set of 21 M dwarfs and brown dwarfs. The line list includes the detection of the Na i D lines in emission for a L3 dwarf.